FreeSurfer Linux Installation

Viewing contents

To view the contents of a distribution, once downloaded, type:

tar tzf freesurfer-Linux-<platform>-<release>-full.tar.gz

replacing <platform>-<release> with whatever is appropriate. The 'tar tzf' command will not install the contents, just show the contents of the tar.gz file.

Installing contents

The tar.gz file will extract to a directory called 'freesurfer'. To install, mv the tar.gz file to whereever you wish to install freesurfer, and type:

tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz

Again, replacing <platform>-<release> with your Linux variant.

MINC toolkit perl path fix-up

Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, as root user, type:

mkdir -p /usr/pubsw/bin
cd /usr/pubsw/bin
ln -s `which perl`

Now the MNI tools will find the perl binary on your platform. You can confirm this by typing 'nu_correct', which should return version information (v1.10).

Freesurfer license file

A license file is required to enable the tools. One can be obtained for free by registering at:

http://surfer.nmr.mgh.harvard.edu/registration.html

Upon receiving the license information by email, copy the three lines of the license information to a file named .license (thats DOT license) and copy that file to your $FREESURFER_HOME.

-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
-= FreeSurfer Linux Installation !!! work in progress!!!  =
+= FreeSurfer Linux Installation =
 Line 5:
-. Obtain a license key from http://surfer.nmr.mgh.harvard.edu/registration.html or from a previous installation. If you are using a previous installation, the license file is found in the main freesurfer directory and is called '.license'.
+== Viewing contents ==
 Line 7:
-. cd to the directory just above where you want !FreeSurfer to be installed (the ParentDir). You will need about 1G of space on this disk partition.
+To view the contents of a distribution, once downloaded, type:

{{{

tar tzf freesurfer-Linux-<platform>-<release>-full.tar.gz

}}}

replacing <platform>-<release> with whatever is appropriate.  The 'tar tzf' command will not install the contents, just show the contents of the tar.gz file.
-Line 9:
+Line 13:
-. Enter the command (replacing 'freesurfer.tar.gz' with the actual filename downloaded):
+== Installing contents ==
-Line 11:
+Line 15:
-     `tar xvfz freesurfer.tar.gz`
+The tar.gz file will extract to a directory called 'freesurfer'.  To install, mv the tar.gz file to whereever you wish to install 

freesurfer, and type:

{{{

tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz

}}}

Again, replacing <platform>-<release> with your Linux variant.
-Line 13:
+Line 22:
-This will create a directory called freesurfer, in which will be the following files:
+== MINC toolkit perl path fix-up ==
-Line 15:
+Line 24:
-  `INSTALL`            -- this file[[BR]]

  `license.freesurfer` -- license agreement[[BR]]

  `freesurfer.tar.gz`  -- !FreeSurfer tree[[BR]]

  `talairach.tar.gz`   -- MNI 305 talairach brain[[BR]]

  `bert.raw.tar.gz`    -- !FreeSurfer tutorial data[[BR]]

  `bert.func.tar.gz`   -- !FreeSurfer functional tutorial data[[BR]]

  `bert.recon.tar.gz`  -- reconstructed !FreeSurfer tutorial data[[BR]]

  `average7.tar.gz`    -- contains average labels for checking spherical morph[[BR]]
+Some of the MNI tools currently contain hard-coded paths to perl.  To fix this situation, as root user, type:

{{{

mkdir -p /usr/pubsw/bin

cd /usr/pubsw/bin

ln -s `which perl`

}}}
-Line 24:
+Line 31:
-. The default subjects directory (the directory in which your subjects' data will be placed) is freesurfer/subjects. You may wish set to up your installation differently, e.g. if you have a large external hard drive you want to use for subject data. See the [wiki:Self:SetupConfiguration 'Setup and Configuration'] section for details.  Regardless, cd into your subjects directory (the default is called 'subjects', located within the freesurfer installation directory) and enter the commands:
+Now the MNI tools will find the perl binary on your platform. You can confirm this by typing 'nu_correct', which should 

return version information (v1.10).
-Line 26:
+Line 34:
-     `tar xvfz DISTDIR/average7.tar.gz` [[BR]]

     `tar xvfz DISTDIR/bert.recon.tar.gz`[[BR]]

     `tar xvfz DISTDIR/talairach.tar.gz`
+== Freesurfer license file ==
-Line 30:
+Line 36:
-This will populate your subjects directory with 'average7', the sample data set 'bert', and the MINC atlas subject 'talairach'.
+A license file is required to enable the tools.  One can be 

obtained for free by registering at:
-Line 32:
+Line 39:
-== MINC installation ==
+http://surfer.nmr.mgh.harvard.edu/registration.html
-Line 34:
+Line 41:
-!FreeSurfer uses some of the tools developed at the Montreal Neurological Institue (MNI) (http://www.bic.mni.mcgill.ca) to align antomical volumes (using minctracc) and to compute the Talairach transform (using mritotal). You must have the MNI tools installed to be able to access this functionality through !FreeSurfer.



The [http://www.bic.mni.mcgill.ca/software/distribution MNI-BIC software distribution page] contains binaries for most platforms.  Note: the Mac OS X FreeSurfer distribution contains the MINC toolkit in its installation.



An alternative is to build the tools required by !FreeSurfer from source.  A special [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz source code bundle], with build scripts, has been prepared by MGH for !FreeSurfer users.  Refer to the [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README.txt README file] for more information on building the MINC toolkit from this source code bundle.
+Upon receiving the license information by email, copy the three

lines of the license information to a file named .license (thats

DOT license) and copy that file to your $FREESURFER_HOME.